CS 882: Advanced Topics in Bioinformatics (Fall 2014)

--History and Frontier of Bioinformatics

Course Information

  • First class will be on Thursday, Sept. 10.
  • Time and Location:
    Every Thursday, 1 - 3:50 pm. DC2568.
    Bin Ma
    Office Hours:
    Every Tuesday, Friday 10:30 - 11:30 am, DC2582.

    A strong algorithm background is required to understand a large portion of the course. Prior knowledge about bioinformatics and/or biology is highly recommended.


    No required textbook. Lecture notes and reference research papers will be made available through this website.

    Course Goals and Format:

    The course aims to provide an overall introduction to several important subareas of bioinformatics. It will also provide an in-depth introduction to the new computational proteomics area.

    The reviews will put those problems into the historical background. We will explain:

    • the developments in biology that motivated the formulation of the computational problem.
    • the computational problems formulated, their variations and solutions.
    • the impact of the bioinformatics solution in further advancing biology.

    The course will start with a series of lectures by the instructor that cover the following topics:

    • The emerging of bioinformatics
    • Sequence comparison
    • Genome sequencing
    • Computational proteomics (an in-depth introduction)
    Then each student is required to do a similar lecture on a specific bioinformatics area, sub area, or reserach problem.

    Marking Scheme:
    Class attendance and participation: 20%; Review: 80% (40% written + 40% presentation)

    Course Outline

    Course Notes

    1. Emerging of Bioinformatics. (1.pdf)

    A superficial overview of the developments in genetics and biology that lead to the study of bioinformatics (computational biology).

    2. Sequence Comparison. (2.pdf)

    This is an updated version of the slides .

    Sequence comparison is the first problem studied in computational biology. Yet it completely changed the modern biology study. This section covers from 1960s to early 2000s. We will learn the problem formulated and algorithm developed by the bioinformatics pioneers.

    3. Genome Sequencing. (3.pdf)

    Genome sequencing produced the first type of large biomolecular dataset that justified the existence of bioinformatics -- a human was not anymore capable of handling the large dataset. On the other hand, large genome sequencing was not possible without the availability of bioinformatics tools. We will examine how the develpments in biology experiments and bioinformatics interwined in the development of genome sequencing since 1980s. Until today, this joint development is still continuings in the "Next Generation Sequencing". NGS is the very frontier of bioinformatics today.

    4. Computational Proteomics (4.pdf)

    Proteomics is another perfect example of the co-development of new measurements in biology and bioinformatics. In very late of 1980s the experimental scientist made it possible to ionize intact proteins (putting electric charges on proteins); and then a computer program changed everything ... proteomics emerged. Proteomics is another frontier of bioinformatics today.